The ability to pinpoint the causal genetic variation and interpret the related developmental processes that lead to phenotypic variation is critical to our knowledge of how to treat and prevent human disease, improve crop yields, and to increase our understanding of evolutionary processes such as natural selection, adaptation, and speciation. Here we use several techniques to identify the genetic basis of variation in cell anisotropy affecting spur length, an adaptive trait in the genus Aquilegia. Several methods will be used to identify candidate loci for spur length variation. First, whole genome sequencing of 276 F2 progeny of a cross between the medium spurred species, Aquilegia formosa, and the long spurred species A. pubescens, will be used to map QTL for spur length. We will then use natural hybrid zones between A. formosa and A. pubescens to take advantage of increased marker recombination in advanced generation hybrids (relative to the F2 progeny used for QTL mapping) to narrow the genomic regions associated with differences in spur length. For these admixed individuals, methods of genome capture will be implemented to selectively sequence genomic regions associated with the previously identified QTL for marker genotyping and association analyses. We will also perform genome-wide scans for selection to identify regions of the genome in each species that show signs of positive selection. Combining these data will allow us to come up with a more refined list of candidate loci affecting spur length than any method independently. Gene expression and functional analyses will then be conducted on candidate genes to confirm and further comprehend their roles in the development of cell anisotropy and spur length variation. These analyses will provide basic information on the genetic basis of adaptive traits, including estimates for the number and genomic distribution of loci involved, the effect size of loci, and whether adaptive trait variation is caused by regulator or structural genetic changes.